A gene is considered a candidate gene for obesity or type 2 diabetes (T2D) in Pima Indians if 1) it has a known physiological function in a pathway relevant to T2D/obesity or 2) it is associated with diabetes/obesity in another human population or in an animal model. In the past year we have directly sequenced and genotyped all tagging variants in several physiologic candidate genes for association analysis with BMI or T2D. Genotyping was performed in two large population-based samples of individuals collected from the Gila River Indian Community. Rare variants in genes along the Leptin/Melanocortin pathway cause severe monogenic obesity in childhood; therfore, genes along this pathway have been sequenced and genotyped as candidate genes for obesity in Pima Indians. Within the past year, we have studied the genes MC4R,Sim1 and BDNF.We have previously reported on rare coding variation in MC4R, but have now investigated whether common, non-coding variation at this locus also affects risk for obesity. A common haplotype (frequency=0.35) from two independent signals in MC4R was identified which provided evidence for association with BMI in American Indians during both adulthood and childhood. Our longitudinal data with repeated BMI measures allowed a comprehensive assessment for the effect of MC4R on obesity risk over lifetime (age 5-50 years). We also identified a MC4R promoter variant that affects expression in vitro, and showed that it influences risk of obesity in part through a propensity for increased food intake and decreased energy expenditure. Our study was the first to report association between a common variant and ad libitum food intake using an automated vending machine paradigm in a clinical research unit, which provides a more objective, reproducible and accurate measure of food intake than that afforded by methods based on self-report. We also analyzed the gene BDNF and perfomed a meta-analysis of our data with that of other another group studying obesity in Caucasian children. Glucokinase (GCK) plays a role in glucose metabolism and glucose-stimulated insulin secretion. Rare mutations in GCK cause maturity-onset diabetes of the young (MODY). We investigated whether common variation (mAF &#8805;0.01) in GCK is associated with metabolic traits and T2D and identified a novel 3UTR SNP chr7:44184184-G/A that associated with the rate of carbohydrate oxidation postabsorptively (&#946;=0.22 mg kgEMBS-1 min-1, p=0.005) and during a hyperinsulinemic, euglycemic clamp (&#946;=0.24 mg kgEMBS-1 min-1, p=0.0002), the rate of carbohydrate oxidation in a respiratory chamber (&#946;=311 kJ/day, p=0.03) and 24-h energy expenditure that was attributable to the thermic effect of food (&#946;=520 kJ/day, p=3.39x10-6). This 3UTR SNP was also associated with diabetes OR=1.36(1.11, 1.65), p=0.002, where the A-allele (AF=0.05) was associated with a lower rate of carbohydrate oxidation, lower 24-h energy expenditure and higher risk for diabetes. In a Cox proportional hazards model, a lower than the mean rate of insulin-stimulated carbohydrate oxidation at baseline predicted a higher risk for developing diabetes than those above the mean HRR=2.2(1.3-3.6), p=0.002. We have also investigated genes that are not physiologic candidates for T2D, but were identified as T2D loci in genome-wide assocation studies in other ethnic groups. For example, a recent trans-ancestry meta-analysis GWAS (DIAGRAM) identified seven new loci associated with T2D. We assessed replication of the seven lead SNPs and further evaluated these loci for additional signals in American Indians. Two of the seven newly identified variants had nominal evidence for association with T2D and related traits in American Indians. However, within the LPP locus, a different variant was identified in American Indians which suggests that more than one region may harbor T2D associated variants at this locus. Similarily, genetic variants in SLC16A11 were recently reported to be associated with T2D in Mexican and other Latin American populations. The diabetes risk haplotype had a frequency of 50% in Native Americans from Mexico, but was rare in Europeans and Africans. We analyzed SLC16A11 in 12,811 North American Indians and found that the diabetes risk haplotype, tagged by the rs75493593 A allele, was nominally associated with T2D; however, there was a strong interaction with BMI such that the diabetes association was stronger in leaner individuals. Rs75493593 was also strongly associated with BMI in individuals with T2D (P = 3.4 10-15) but not in non-diabetic individuals (P = 0.77). Longitudinal analyses suggest that this is due, in part, to an association of the A allele with greater weight loss following diabetes onset. Analyses of global gene expression data from adipose, skeletal muscle, and whole blood provide evidence that rs75493593 is associated with expression of the nearby RNASEK gene, suggesting that RNASEK expression may mediate the effect of genotype on diabetes.